Group 4 Project Presentation: Gene Expression in Bone Marrow Cells
2024-12-03
Introduction
- The myelodysplastic syndromes (MDS) are a diverse set of cancers in the bone marrow.
- The bone marrow consists of several cell types - amongst these hematopoietic stem cells and progenitor cells.
- Gene expression analysis of specific cell fractions derived from the bone marrow could reveal potential targets of therapy and immune evasive mechanisms.
Materials and methods: Data Retrieval and Cleaning
Flowchart of data aquisition and inital tidying
Methods: Gene Mapping, Cleanup and DESeq2 Analysis
Flowchart of data augmentation
Sample compositions
(A) Overall cellular composition of the MDS patient samples as well as healthy donors
(B) The following plots depicts the total number as well as the fraction of MDS and HD samples that contain the srsf2 and sf3b1 mutations within the various cellular compartments.
Distribution of counts
The histograms above illustrate gene counts from both MDS patients and healthy donors, displayed before and after normalization.
The impact of normalization appears subtle. However, it is noticeable that the overall gene counts in MDS patients are comparatively higher than those in healthy donors.
Clustering using PCA on all cells and on HSC
Clustering analysis using K-means (k = 4)
Differential gene expression: All samples and HSC
Differential gene expression across the different cell populations - MDS vs. HD
